6-15790919-C-G

Variant names:

• chr6-15790919-C-G
• rs191986
• ENST00000806821.1:n.232C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000806821.1(ENSG00000289953):​n.232C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 152,058 control chromosomes in the GnomAD database, including 16,539 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (16539 hom., cov: 33)
• Consequence: ENSG00000289953 ENST00000806821.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 1 publications found

Genes affected

ENSG00000289953 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289953	ENST00000806821.1	n.232C>G		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000289953	ENST00000806822.1	n.246C>G		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000289953	ENST00000806826.1	n.246C>G		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68271 AN: 151942 Hom.: 16528 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.0640

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.450

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.449 AC: 68316 AN: 152058 Hom.: 16539 Cov.: 33 AF XY: 0.444 AC XY: 32982 AN XY: 74330

African (AFR) AF: 0.315 AC: 13046 AN: 41480

American (AMR) AF: 0.438 AC: 6689 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1906 AN: 3468

East Asian (EAS) AF: 0.0640 AC: 331 AN: 5172

South Asian (SAS) AF: 0.297 AC: 1430 AN: 4810

European-Finnish (FIN) AF: 0.566 AC: 5976 AN: 10558

Middle Eastern (MID) AF: 0.414 AC: 120 AN: 290

European-Non Finnish (NFE) AF: 0.550 AC: 37412 AN: 67976

Other (OTH) AF: 0.445 AC: 939 AN: 2112

Alfa AF: 0.371 Hom.: 1033

Bravo AF: 0.441

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.45
PhyloP100		-0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs191986; hg19: chr6-15791150;